Resource

Id: gene_properties/gene_scores/LOEUF
Type: gene_score
Version: 0
Summary:

Degree of intolerance to predicted Loss-of-Function (pLoF) variation

Description:

Introduction

Degree of intolerance to pLoF variation in each gene is assessed using the continuous metric of the observed/expected ratio. A confidence interval is estimated around the ratio. The loss-of-function observed/expected upper bound fraction (LOEUF) is the 90% upper bound of this confidence interval.

Score definitions

Low scores or ranks indicate intolerance to loss of function mutations.

Processing Details

Supplementary Data, Table 11 downloaded on 2024 May 5 from https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7334197/#MOESM1.

DataPrep.py utilizes only scores for canonical transcripts (column canonical = TRUE). The 'oe_lof_upper' column in the downloaded file is used for LOEUF scores. LOEUF_ranks are calculated based on LOEUF scores. Resulting file LOEUF_scores.csv.gz has 3 columns: gene, LOEUF score, LOEUF rank.

Labels:

Scores

ID Type Description Histograms Range
LOEUF
90% upper bound for the confidence interval for observed/expected pLoF variation ratio
Small values desc: intolerant to pLoF variation
Large values desc: tolerant to pLoF variation
LOEUF
[0.030, 1.996]
LOEUF_rank
Gene ranks after sorting by LOEUF scores
Small values desc: intolerant to pLoF variation
Large values desc: tolerant to pLoF variation
LOEUF_rank
[1.000, 19197.000]

Files

Filename Size md5
DataPrep.py 1.09 KB ec139d6ccbaa42ca8aa8c303b497155e
LOEUF_scores.csv.gz 129.89 KB 2de3bb891f944af4d9cc3ac642294e99
genomic_resource.yaml 1.79 KB b3855f4060b82193109415a205a64f47
supplementary_dataset_11_full_constraint_metrics.tsv.gz 13.02 MB 338a3ed667290813cafbb72eabcba2e0
statistics/